I have now spent quite some time on this and finally I can reproduce this issue. It happens nearly every time I crossfade between 2 multitrack songs with 6 tracks wav files each and where the second song has a sample rate of 48kHz. Once the problems start they occur every time I play a 48kHz multitrack song. They disappear if I close and restart the app via the task switcher.
I have tried lots of approaches to get rid of this issue but nothing seems to work out. I guess this must be a bug in the Apple audio framework. I will try to write some simple test code and send it with a bug report to Apple.
The audio engine in Stage Traxx runs with a fixed 44.1kHz sample rate and as far as I can tell this issue only happens for songs that have audio files running with another samplerate than 44.1kHz. So my suggestion is that especially when running multitrack songs, make sure that your audio files only use a sample rate of 44.1kHz. I will also add this hint to the manual.